# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 02:46:22 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: 3-(2-pyrimidin-4-ylethyl)-1~{H}-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C(Cc1c[nH]c2ccccc12)c3ccncn3
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 UMZ  UMZ  "3-(2-pyrimidin-4-ylethyl)-1~{H}-indole"
  ligand  30  17  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UMZ
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 UMZ  N1   N  N     0  -0.397  -14.1251  16.5189  4.2235
 UMZ  C7   C  CH2   0  -0.496  -10.1633  17.7134  3.3620
 UMZ  C8   C  CR6   0   0.287  -11.5739  17.3359  3.6867
 UMZ  N2   N  N     0  -0.410  -11.8257  16.0465  3.9167
 UMZ  C9   C  CR16  0  -0.357  -12.6025  18.2699  3.7158
 UMZ  C1   C  CR16  0  -0.282   -4.6339  16.0028  2.7907
 UMZ  C5   C  CR5   0   0.015   -8.3477  17.5483  1.6274
 UMZ  C6   C  CH2   0  -0.531   -9.7773  17.2638  1.9426
 UMZ  N3   N  NR15  0  -0.688   -6.4917  18.4968  0.7996
 UMZ  C4   C  CR56  0   0.029   -7.2022  16.8676  2.1573
 UMZ  C3   C  CR16  0  -0.374   -7.0370  15.7853  3.0296
 UMZ  C2   C  CR16  0  -0.266   -5.7585  15.3634  3.3387
 UMZ  C10  C  CR16  0  -0.025  -13.8743  17.8032  3.9939
 UMZ  C11  C  CR16  0   0.042  -13.0787  15.7082  4.1704
 UMZ  C12  C  CR15  0  -0.088   -7.8590  18.5278  0.8103
 UMZ  C13  C  CR56  0   0.354   -6.0578  17.4930  1.6141
 UMZ  C14  C  CR16  0  -0.304   -4.7656  17.0707  1.9239
 UMZ  H6   H  HCH2  0   0.261   -9.4944  17.2432  4.0863
 UMZ  H7   H  HCH2  0   0.256  -10.0349  18.7931  3.4494
 UMZ  H8   H  HCR6  0   0.276  -12.4176  19.3190  3.5314
 UMZ  H5   H  HCH2  0   0.252  -10.4243  17.7663  1.2197
 UMZ  H4   H  HCH2  0   0.244   -9.9777  16.1931  1.8463
 UMZ  H12  H  HNR5  0   0.406   -5.9033  19.1175  0.2692
 UMZ  H3   H  HCR6  0   0.239   -7.8981  15.2849  3.4569
 UMZ  H2   H  HCR6  0   0.242   -5.6164  14.5280  4.0122
 UMZ  H9   H  HCR6  0   0.277  -14.7179  18.4836  4.0338
 UMZ  H10  H  HCR6  0   0.258  -13.2689  14.6563  4.3569
 UMZ  H11  H  HCR5  0   0.278   -8.3961  19.2581  0.2248
 UMZ  H13  H  HCR6  0   0.256   -3.8968  17.5597  1.5013
 UMZ  H1   H  HCR6  0   0.246   -3.6440  15.6507  3.0513

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 UMZ  N3   C12  aromatic  1.368  0.020  1.368
 UMZ  N3   C13  aromatic  1.364  0.020  1.364
 UMZ  C12  C5   aromatic  1.366  0.020  1.366
 UMZ  C5   C6   single    1.491  0.020  1.491
 UMZ  C5   C4   aromatic  1.434  0.020  1.434
 UMZ  C13  C14  aromatic  1.394  0.020  1.394
 UMZ  C13  C4   aromatic  1.413  0.020  1.413
 UMZ  C6   C7   single    1.538  0.020  1.538
 UMZ  C14  C1   aromatic  1.382  0.020  1.382
 UMZ  C4   C3   aromatic  1.400  0.020  1.400
 UMZ  C1   C2   aromatic  1.405  0.020  1.405
 UMZ  C3   C2   aromatic  1.381  0.020  1.381
 UMZ  C7   C8   single    1.496  0.020  1.496
 UMZ  C8   C9   aromatic  1.390  0.020  1.390
 UMZ  C8   N2   aromatic  1.334  0.020  1.334
 UMZ  C9   C10  aromatic  1.383  0.020  1.383
 UMZ  N2   C11  aromatic  1.322  0.020  1.322
 UMZ  C10  N1   aromatic  1.329  0.020  1.329
 UMZ  C11  N1   aromatic  1.325  0.020  1.325
 UMZ  C7   H6   single    0.970  0.020  1.090
 UMZ  C7   H7   single    0.970  0.020  1.090
 UMZ  C9   H8   single    0.930  0.020  1.080
 UMZ  C1   H1   single    0.930  0.020  1.080
 UMZ  C6   H5   single    0.970  0.020  1.090
 UMZ  C6   H4   single    0.970  0.020  1.090
 UMZ  N3   H12  single    0.860  0.020  1.020
 UMZ  C3   H3   single    0.930  0.020  1.080
 UMZ  C2   H2   single    0.930  0.020  1.080
 UMZ  C10  H9   single    0.930  0.020  1.080
 UMZ  C11  H10  single    0.930  0.020  1.080
 UMZ  C12  H11  single    0.930  0.020  1.080
 UMZ  C14  H13  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 UMZ  C11  N1   C10  115.81  3.000
 UMZ  H7   C7   H6   107.51  3.000
 UMZ  H7   C7   C6   109.50  3.000
 UMZ  H6   C7   C6   109.41  3.000
 UMZ  H7   C7   C8   110.09  3.000
 UMZ  H6   C7   C8   108.96  3.000
 UMZ  C6   C7   C8   111.29  3.000
 UMZ  C9   C8   N2   120.42  3.000
 UMZ  N2   C8   C7   117.35  3.000
 UMZ  C9   C8   C7   122.20  3.000
 UMZ  C11  N2   C8   117.34  3.000
 UMZ  H8   C9   C10  121.27  3.000
 UMZ  H8   C9   C8   121.47  3.000
 UMZ  C10  C9   C8   117.26  3.000
 UMZ  H1   C1   C14  119.31  3.000
 UMZ  H1   C1   C2   119.35  3.000
 UMZ  C14  C1   C2   121.34  3.000
 UMZ  C12  C5   C4   106.00  3.000
 UMZ  C4   C5   C6   126.66  3.000
 UMZ  C12  C5   C6   127.32  3.000
 UMZ  H4   C6   H5   106.47  3.000
 UMZ  H4   C6   C5   110.11  3.000
 UMZ  H5   C6   C5   109.88  3.000
 UMZ  H4   C6   C7   108.75  3.000
 UMZ  H5   C6   C7   109.12  3.000
 UMZ  C5   C6   C7   112.32  3.000
 UMZ  H12  N3   C13  125.65  3.000
 UMZ  H12  N3   C12  125.08  3.000
 UMZ  C13  N3   C12  109.27  3.000
 UMZ  C13  C4   C3   119.09  3.000
 UMZ  C3   C4   C5   133.75  3.000
 UMZ  C13  C4   C5   107.15  3.000
 UMZ  H3   C3   C2   120.41  3.000
 UMZ  H3   C3   C4   120.59  3.000
 UMZ  C2   C3   C4   119.00  3.000
 UMZ  H2   C2   C3   119.77  3.000
 UMZ  H2   C2   C1   119.26  3.000
 UMZ  C3   C2   C1   120.97  3.000
 UMZ  H9   C10  C9   120.73  3.000
 UMZ  H9   C10  N1   116.95  3.000
 UMZ  C9   C10  N1   122.32  3.000
 UMZ  H10  C11  N2   116.55  3.000
 UMZ  H10  C11  N1   116.61  3.000
 UMZ  N2   C11  N1   126.84  3.000
 UMZ  H11  C12  N3   120.57  3.000
 UMZ  H11  C12  C5   129.17  3.000
 UMZ  N3   C12  C5   110.25  3.000
 UMZ  C14  C13  C4   122.09  3.000
 UMZ  C4   C13  N3   107.32  3.000
 UMZ  C14  C13  N3   130.58  3.000
 UMZ  H13  C14  C13  121.34  3.000
 UMZ  H13  C14  C1   121.16  3.000
 UMZ  C13  C14  C1   117.50  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 UMZ  CONST_01  C8   C9   C10  N1      0.00   0.0  0
 UMZ  CONST_02  C8   N2   C11  N1      0.00   0.0  0
 UMZ  CONST_03  C10  C9   C8   N2      0.00   0.0  0
 UMZ  CONST_04  C10  N1   C11  N2      0.00   0.0  0
 UMZ  CONST_05  C11  N2   C8   C9      0.00   0.0  0
 UMZ  CONST_06  C11  N1   C10  C9      0.00   0.0  0
 UMZ  CONST_07  N3   C13  C14  C1    180.00   0.0  0
 UMZ  CONST_08  C4   C13  C14  C1      0.00   0.0  0
 UMZ  CONST_09  C4   C3   C2   C1      0.00   0.0  0
 UMZ  CONST_10  C13  N3   C12  C5      0.00   0.0  0
 UMZ  CONST_11  N3   C13  C4   C5      0.00   0.0  0
 UMZ  CONST_12  C14  C13  C4   C5    180.00   0.0  0
 UMZ  CONST_13  C2   C3   C4   C5    180.00   0.0  0
 UMZ  CONST_14  C4   C5   C12  N3      0.00   0.0  0
 UMZ  CONST_15  C3   C4   C13  N3    180.00   0.0  0
 UMZ  CONST_16  C12  N3   C13  C4      0.00   0.0  0
 UMZ  CONST_17  C12  C5   C4   C3    180.00   0.0  0
 UMZ  CONST_18  C14  C13  C4   C3      0.00   0.0  0
 UMZ  CONST_19  C14  C1   C2   C3      0.00   0.0  0
 UMZ  CONST_20  C13  C14  C1   C2      0.00   0.0  0
 UMZ  CONST_21  C13  C4   C3   C2      0.00   0.0  0
 UMZ  CONST_22  C14  C13  N3   C12   180.00   0.0  0
 UMZ  CONST_23  C13  C4   C5   C12     0.00   0.0  0
 UMZ  CONST_24  C10  C9   C8   C7    180.00   0.0  0
 UMZ  CONST_25  C11  N2   C8   C7    180.00   0.0  0
 UMZ  CONST_26  N3   C12  C5   C6    180.00   0.0  0
 UMZ  CONST_27  C13  C4   C5   C6    180.00   0.0  0
 UMZ  CONST_28  C3   C4   C5   C6      0.00   0.0  0
 UMZ  CONST_29  H8   C9   C10  N1    180.00   0.0  0
 UMZ  CONST_30  H9   C10  C9   C8    180.00   0.0  0
 UMZ  CONST_31  H10  C11  N2   C8    180.00   0.0  0
 UMZ  CONST_32  H8   C9   C8   N2    180.00   0.0  0
 UMZ  CONST_33  H3   C3   C2   C1    180.00   0.0  0
 UMZ  CONST_34  H12  N3   C12  C5    180.00   0.0  0
 UMZ  CONST_35  H3   C3   C4   C5      0.00   0.0  0
 UMZ  CONST_36  H13  C14  C13  N3      0.00   0.0  0
 UMZ  CONST_37  H11  C12  C5   C4    180.00   0.0  0
 UMZ  CONST_38  H12  N3   C13  C4    180.00   0.0  0
 UMZ  CONST_39  H13  C14  C13  C4    180.00   0.0  0
 UMZ  CONST_40  H2   C2   C3   C4    180.00   0.0  0
 UMZ  CONST_41  H1   C1   C2   C3    180.00   0.0  0
 UMZ  CONST_42  H13  C14  C1   C2    180.00   0.0  0
 UMZ  CONST_43  H10  C11  N1   C10   180.00   0.0  0
 UMZ  CONST_44  H9   C10  N1   C11   180.00   0.0  0
 UMZ  CONST_45  H11  C12  N3   C13   180.00   0.0  0
 UMZ  CONST_46  H1   C1   C14  C13   180.00   0.0  0
 UMZ  CONST_47  H3   C3   C4   C13   180.00   0.0  0
 UMZ  CONST_48  H12  N3   C13  C14     0.00   0.0  0
 UMZ  CONST_49  H2   C2   C1   C14   180.00   0.0  0
 UMZ  Var_01    C12  C5   C6   C7   -105.93  30.0  2
 UMZ  Var_02    C4   C5   C6   C7     72.06  30.0  2
 UMZ  Var_03    C5   C6   C7   C8   -176.22  30.0  2
 UMZ  Var_04    C6   C7   C8   N2     72.93  30.0  1
 UMZ  Var_05    C6   C7   C8   C9   -105.30  30.0  1
 UMZ  Var_06    H6   C7   C8   N2    -47.80  30.0  1
 UMZ  Var_07    H7   C7   C8   N2   -165.47  30.0  1
 UMZ  Var_08    H6   C7   C8   C9    133.96  30.0  1
 UMZ  Var_09    H7   C7   C8   C9     16.29  30.0  1
 UMZ  Var_10    H5   C6   C5   C4   -166.27  30.0  2
 UMZ  Var_11    H4   C6   C5   C4    -49.30  30.0  2
 UMZ  Var_12    H5   C6   C5   C12    15.74  30.0  2
 UMZ  Var_13    H4   C6   C5   C12   132.71  30.0  2
 UMZ  Var_14    H5   C6   C7   C8     61.68  30.0  2
 UMZ  Var_15    H4   C6   C7   C8    -54.09  30.0  2
 UMZ  Var_16    H6   C7   C6   C5    -55.75  30.0  3
 UMZ  Var_17    H7   C7   C6   C5     61.84  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 UMZ  plan-1  N1   0.020
 UMZ  plan-1  C7   0.020
 UMZ  plan-1  C8   0.020
 UMZ  plan-1  N2   0.020
 UMZ  plan-1  C9   0.020
 UMZ  plan-1  C10  0.020
 UMZ  plan-1  C11  0.020
 UMZ  plan-1  H8   0.020
 UMZ  plan-1  H9   0.020
 UMZ  plan-1  H10  0.020
 UMZ  plan-2  C1   0.020
 UMZ  plan-2  C5   0.020
 UMZ  plan-2  C6   0.020
 UMZ  plan-2  N3   0.020
 UMZ  plan-2  C4   0.020
 UMZ  plan-2  C3   0.020
 UMZ  plan-2  C2   0.020
 UMZ  plan-2  C12  0.020
 UMZ  plan-2  C13  0.020
 UMZ  plan-2  C14  0.020
 UMZ  plan-2  H12  0.020
 UMZ  plan-2  H3   0.020
 UMZ  plan-2  H2   0.020
 UMZ  plan-2  H11  0.020
 UMZ  plan-2  H13  0.020
 UMZ  plan-2  H1   0.020

